PXD012312

PXD012312 is an original dataset announced via ProteomeXchange.

Title	Lessons from Two Design-Build-Test-Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning
Description	The Design–Build–Test–Learn (DBTL) cycle, facilitated by exponentially improving capabilities in synthetic biology, is an increasingly adopted metabolic engineering framework that represents a more systematic and efficient approach to strain development than historical efforts in biofuels and bio-based products. Here, we report on implementation of two DBTL cycles to optimize 1-dodecanol production from glucose using 60 engineered E. coli MG1655 strains. The first DBTL cycle employed a simple strategy to learn efficiently from a relatively small number of strains (36), wherein only the choice of ribosome-binding sites and an acyl-ACP/acyl-CoA reductase were modulated in a single pathway operon including genes encoding a thioesterase (UcFatB1), an acyl-ACP/acyl-CoA reductase (Maqu_2507, Maqu_2220, or Acr1), and an acyl-CoA synthetase (FadD). Measured variables included concentrations of dodecanol and all proteins in the engineered pathway. We used the data produced in the first DBTL cycle to train several machine-learning algorithms and to suggest protein profiles for the second DBTL cycle that would increase production. These strategies resulted in a 21% increase in dodecanol titer in Cycle 2 (up to 0.83 g/L, which is more than 6-fold greater than previously reported batch values for minimal medium). Beyond specific lessons learned about optimizing dodecanol titer in E. coli, this study had findings of broader relevance across synthetic biology applications, such as the importance of sequencing checks on plasmids in production strains as well as in cloning strains, and the critical need for more accurate protein expression predictive tools.
HostingRepository	PanoramaPublic
AnnounceDate	2019-05-16
AnnouncementXML	Submission_2019-05-16_13:58:56.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Chris Petzold
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	Carbamidomethyl
Instrument	6460 Triple Quadrupole LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2019-01-11 15:42:16	ID requested
⏵ 1	2019-05-16 13:58:57	announced

Opgenorth P, Costello Z, Okada T, Goyal G, Chen Y, Gin J, Benites V, de Raad M, Northen TR, Deng K, Deutsch S, Baidoo EEK, Petzold CJ, Hillson NJ, Garcia Martin H, Beller HR, Lessons from Two Design-Build-Test-Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning. ACS Synth Biol, 8(6):1337-1351(2019) [pubmed]

submitter keyword: Synthetic biology, Metabolic engineering, Protoemics, Metabolomics, Machine Learning

Chris Petzold
contact affiliation	Lawrence Berkeley National Laboratory
contact email	cjpetzold@lbl.gov
lab head
Chris Petzold
contact affiliation	Lawrence Berkeley National Laboratory
contact email	cjpetzold@lbl.gov
dataset submitter

Panorama Public dataset URI